This dataset contains the raw and pre-processed microscopy images of hematopoietic stem cell (HSC) nuclei stained with DAPI described in the paper "Targeting RhoA activity rejuvenates aged haematopoietic stem cells" by Mejía-Ramírez et al. The code used to process and analyse the images can be found here: https://github.com/biomedical-data-science/hsc_rhoa. This dataset also contains the original Western Blot images. Moreover, it contains the code used to analyse the bulk ATAC, bulk RNA, and scRNA sequencing data, the raw count matrices and the main output obtained from running the code. The raw FASTQ files can be found under the GEO accession number GSE233989. The code is in an easily reproducible format, as bash and R scripts and Rmarkdown and Jupyter notebooks that contain comments that describe all the steps in the analysis. To reproduce it, download all the files in the repository directory "ATACandRNAseq_dataAnalysis_reproducibleCode" and, for each analysis, follow the steps in the "Readme.txt" file.